HELP! PlayerPrefs.DeleteAll(); caused my controller to not be recognized in the editor. Unplayable.

I'm working on a project with controller support. The controller was working just fine until I used the PlayerPrefs.DeleteAll() function. Now it doesn't recognize my controller in the editor. It works fine in other projects, and it works fine when I use Build & Run. I use a PS3 controller with an XInput wrapper, so basically an XBox 360 controller. (And like I said, it works fine in everything else, so it's not a driver issue.)

Is there some kind of data in PlayerPrefs that I deleted that caused this? I've been searching for hours with no answers, and I'm starting to despair, as now my project is unplayable in the editor. Maybe I can re-map controls to my controller for the editor somehow? While in the editor, I can still jump by clicking the mouse, but I can't get any controls to make him move. I've been unable to make him move with keyboard buttons for a while, though, ever since I got the controller to work. Not sure why.

Please help. I'm kinda freaking out a little over here, since I think I borked my project... I have some backups I can jury-rig a solution out of one way or another, but I'd really hate it to come to that... Thank you.

Edit: Now it's happening even on new projects! But only after closing and re-opening a scene. When I first create a project, I create a scene and add a plane and the Third Person Controller from Standard Assets. I hit Play, and everything works fine. I can walk around like normal. Then I save the scene, close Unity and open it again, hit Play, and nothing works. Not the controller, not the keyboard. I don't know if the mouse works, but it does in my other project where "jump" is still mapped to Left Click. What the hell is going on?